Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for EIF4E
Basic gene info.Gene symbolEIF4E
Gene nameeukaryotic translation initiation factor 4E
SynonymsAUTS19|CBP|EIF4E1|EIF4EL1|EIF4F
CytomapUCSC genome browser: 4q23
Genomic locationchr4 :99799606-99850243
Type of geneprotein-coding
RefGenesNM_001130678.1,
NM_001130679.1,NM_001968.3,
Ensembl idENSG00000151247
DescriptioneIF-4EeIF-4F 25 kDa subuniteukaryotic translation initiation factor 4E-like 1mRNA cap-binding protein
Modification date20141207
dbXrefs MIM : 133440
HGNC : HGNC
HPRD : 00591
ProteinUniProt: P06730
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF4E
BioGPS: 1977
Gene Expression Atlas: ENSG00000151247
The Human Protein Atlas: ENSG00000151247
PathwayNCI Pathway Interaction Database: EIF4E
KEGG: EIF4E
REACTOME: EIF4E
ConsensusPathDB
Pathway Commons: EIF4E
MetabolismMetaCyc: EIF4E
HUMANCyc: EIF4E
RegulationEnsembl's Regulation: ENSG00000151247
miRBase: chr4 :99,799,606-99,850,243
TargetScan: NM_001130678
cisRED: ENSG00000151247
ContextiHOP: EIF4E
cancer metabolism search in PubMed: EIF4E
UCL Cancer Institute: EIF4E
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF4E in cancer cell metabolism1. Chatterjee A, Mukhopadhyay S, Tung K, Patel D, Foster DA (2015) Rapamycin-induced G1 cell cycle arrest employs both TGF-beta and Rb pathways. Cancer Lett 360: 134-140. doi: 10.1016/j.canlet.2015.01.043. pmid: 4415112. go to article
2. Su X, Yu Y, Zhong Y, Giannopoulou EG, Hu X, et al. (2015) Interferon-gamma regulates cellular metabolism and mRNA translation to potentiate macrophage activation. Nat Immunol. doi: 10.1038/ni.3205. go to article
3. Li SH, Chen CH, Lu HI, Huang WT, Tien WY, et al. (2015) Phosphorylated p70S6K expression is an independent prognosticator for patients with esophageal squamous cell carcinoma. Surgery 157: 570-580. doi: 10.1016/j.surg.2014.10.014. go to article

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Phenotypic Information for EIF4E(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF4E
Familial Cancer Database: EIF4E
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 133440; gene.
615091; phenotype.
Orphanet 106; Autism.
DiseaseKEGG Disease: EIF4E
MedGen: EIF4E (Human Medical Genetics with Condition)
ClinVar: EIF4E
PhenotypeMGI: EIF4E (International Mouse Phenotyping Consortium)
PhenomicDB: EIF4E

Mutations for EIF4E
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryEIF4Echr49983709299837112TSPAN5chr49948301399483033
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EIF4E related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF879888ABCA172949107587996107589344EIF4E28848649980980399810001
DA724990EIF4E114849982302599850284UBXN71445433196118683196134267

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=9)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr4:99823101-99823101p.T17T2
chr4:99808251-99808251p.L126L1
chr4:99802262-99802262p.P191A1
chr4:99808254-99808254p.D125D1
chr4:99823113-99823113p.N13K1
chr4:99802265-99802265p.P190S1
chr4:99808316-99808316p.E105K1
chr4:99823128-99823128p.T8T1
chr4:99802300-99802300p.?1
chr4:99808326-99808326p.M101I1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  1    1  31  123 4
# mutation1  1    1  41  123 4
nonsynonymous SNV1       1  3    11 2
synonymous SNV   1       11  112 2
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr4:99823086p.T42T,EIF4E2
chr4:99823101p.T37T,EIF4E2
chr4:99823081p.P210S,EIF4E1
chr4:99802265p.F162F,EIF4E1
chr4:99806186p.R148H,EIF4E1
chr4:99808246p.R148C,EIF4E1
chr4:99823113p.L146L,EIF4E1
chr4:99808247p.D145D,EIF4E1
chr4:99823128p.M121I,EIF4E1
chr4:99808251p.S102C,EIF4E1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for EIF4E in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for EIF4E

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.
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check002.gifProtein Expression Plot (RPPA)
*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

ALG3,ASH2L,BOLA3,BRF2,BUD31,ECE2,EIF4EBP1,
LSM1,LSM4,MRPS2,NPM3,POLR2H,PPAPDC1B,PROSC,
PSMG3,RPL30,SNHG6,SRM,TCEB1,TIMM44,UBE2S
ACSM2B,ASS1,BSG,IZUMO4,C20orf27,EIF4EBP1,FPGS,
GCDH,GLYCTK,MEF2B,MPST,NDRG4,PCBD1,PCYT2,
PDZD7,PMM1,PQLC1,PXMP2,RASL10B,RPLP2,TMEM120A

ASH2L,BRF2,CENPM,CYC1,EIF3I,EIF4EBP1,EIF5A,
EXOSC4,H2AFZ,KRTCAP3,LSM1,MFSD2B,MRPL12,MRTO4,
PROSC,PUSL1,RCC1,RPS6KB2,SRSF9,SRM,ZNF511
AFMID,C19orf48,C9orf142,CCDC34,EIF4EBP1,EXOSC5,FBXW9,
GCAT,MPG,MRPS18A,MRPS26,NAT9,NTHL1,PAFAH1B3,
PPP5C,PRPS2,SLC35B2,SSBP4,SYNGR2,TMED3,YIPF2
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for EIF4E
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P06730; -.
ChemistryChEMBL CHEMBL4848; -.
Organism-specific databasesPharmGKB PA27714; -.
Organism-specific databasesCTD 1977; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01649eukaryotic translation initiation factor 4Eexperimental7-Methyl-Gpppa
DB01960eukaryotic translation initiation factor 4Eexperimental7n-Methyl-8-Hydroguanosine-5'-Diphosphate
DB02716eukaryotic translation initiation factor 4Eexperimental7-Methyl-Guanosine-5'-Triphosphate
DB08217eukaryotic translation initiation factor 4Eexperimental2,2,5,5-TETRAMETHYL-3-(SULFANYLMETHYL)-2,5-DIHYDRO-1H-PYRROL-1-OL
DB00877eukaryotic translation initiation factor 4Eapproved; investigationalSirolimus


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Cross referenced IDs for EIF4E
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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